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Unified Medical Language System® (UMLS®)

2015AB UMLS OMIM Source Information

This page lists specific source data elements and provides information on their representation in the UMLS Metathesaurus.




Skip to: Notes, Summary of Changes, Summary of Source-Provided Files Source-Provided File Details

Summary of Changes:

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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: Summary

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XML records are supplied according to Metathesaurus specifications.

Documentation and Reference

File Name Description
http://www.ncbi.nlm.nih.gov/dtd/NCBI_Mim.mod.dtd XML dtd
http://omim.org/help/faq
FAQ

XML Data

Not included: Data from many tags are not included in Metathesaurus source processing, because they do not contain terminological content.

Source-Provided Data: Details

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The following is a list of elements available for <source> data in XML format

Required Elements:

Element Description Representation
<Mim-entry_mimNumber> Unique identifier
MRCONSO.CODE
MRCONSO.SDUI
<Mim-entry_mimType> The type of OMIM records (asterisk (*), number (#), plus (+), percent (%), caret (^), or none)

An asterisk (*) before an entry number indicates a gene of known sequence.

A number symbol (#) before an entry number indicates that it is a descriptive entry, usually of a phenotype, and does not represent a unique locus. The reason for the use of the #-sign is given in the first paragraph of the entry. Discussion of any gene(s) related to the phenotype resides in another entry(ies) as described in the first paragraph.

A plus sign (+) before an entry number indicates that the entry contains the description of a gene of known sequence and a phenotype.

A percent sign (%) before an entry number indicates that the entry describes a confirmed mendelian phenotype or phenotypic locus for which the underlying molecular basis is not known.

No symbol before an entry number generally indicates a description of a phenotype for which the mendelian basis, although suspected, has not been clearly established or that the separateness of this phenotype from that in another entry is unclear.

A caret symbol (^) before an entry number means the entry no longer exists because it was removed from the database or moved to another entry as indicated.


MRSAT.ATN = "MIMTYPEMEANING"

MRSAT.ATN = "MIMTYPEVALUE"

MRSAT.ATN = "MIMTYPE"

Records with a <Mim-entry_mimType> value of caret (^) are obsolete and are not included in Metathesaurus source processing.

MIMTYPE MIMTYPEVALUE MIMTYPEMEANING
0 none Other, mainly phenotypes with suspected Mendelian basis
1 star Gene with known sequence
3 pound Phenotype description, molecular basis known
4 plus Gene with known sequence and phenotype
5 perc Mendelian phenotype or locus, molecular basis unknown

<Mim-entry_title> Contains the preferred term naming the entry. May include semicolon-separated acronyms. MRCONSO.TTY = "PT", MRCONSO.TTY = "ACR"

Information before the first semicolon is used to create PT atoms. Information following the first semicolon is used to create ACR atoms.

Relationships are created to connect PT to ACR atoms:
REL = SY
RELA = expanded_form_of/has_expanded_form

Optional Elements


Element Description Representation
<Mim-entry_symbol> One or more commas-separated gene symbols MRSAT.ATN = "GENESYMBOL"
<Mim-entry_locus> Notation for one or more loci for the genes associated with this entry MRSAT.ATN = "GENELOCUS"
<Mim-entry_aliases_E> Synonyms/acronyms MRCONSO.TTY = "ETAL"
MRCONSO.TTY = "ACR"

Information before the first semicolon is used to create ETAL atoms

Information after the semicolon is parsed to create ACR atoms

", INCLUDED" is removed from both ETAL and ACR atoms

No ETAL atom is created if the string already exists as an ACR atom

Relationships are created to connect PT to ETAL atoms:
REL = RQ
RELA = has_alias/alias_of

Relationships are created to connect ETAL to ACR atoms:
REL = SY
RELA = expanded_form_of/has_expanded_form
<Mim-entry_included_E> Entry terms/acronyms MRCONSO.TTY = "ET"
MRCONSO.TTY = "ACR"

Information before the first semicolon is used to create ET atoms

Information after the semicolon is parsed to create ACR atoms

The pattern ", INCLUDED" is removed from the string

Relationships are created to connect ET to ACR atoms:
REL = SY
RELA = expanded_form_of/has_expanded_form
<Mim-allelic-variant_number> Allelic variant number (4 digits) MRCONSO.CODE, MRCONSO.SDUI: Appended to the Mim-entry_mimNumber for TTY= PTAV
<Mim-allelic-variant_name> Allelic variant name. Most allelic variants represent disease-producing mutations. A few polymorphisms are included. For most genes, only selected mutations are included as specific entries. MRCONSO.TTY = "PHENO"

Relationships are created to connect PHENO to PTAV atoms:
REL = RO
RELA = phenotype_of/has_phenotype
<Mim-allelic-variant_aliases_E> Allelic variant aliases MRCONSO.TTY = "PHENO_ET"

The pattern ", INCLUDED" is removed from the string

Relationships are created to connect PHENO_ET to PTAV atoms:
REL = RO
RELA = phenotype_of/has_phenotype
<Mim-allelic-variant_mutation><Mim_text_text> The type of mutations which show statistical correlation to the particular disorders. MRCONSO.TTY = "PTAV"

Relationships are created to connect PTAV to PT atoms:
REL = RO
RELA = allelic_variant_of/has_allelic_variant

Relationships are created to connect PTAV to PHENO and PHENO_ET atoms:
REL = RO
RELA = has_phenotype/phenotype_of

The CODE/SDUI has the Mim-allelic-variant_number appended.
<Mim-entry_clinicalSynopsis><Mim-index-term_key> Clinical synopsis header terms MRCONSO.TTY = "HT"

Values are excluded from Metathesaurus source processing if they meet any of the following criteria:
  • Mixed-case/lower-case string. These values have not yet been reviewed by OMIM
  • Have an <Mim-entry_synopsisEditHistory><Mim-date_year> before 1996
  • Do not have a "MIM-entry_synopsisEditHistory" tag
<Mim-entry_clinicalSynopsis><Mim-index-term_terms_E> Clinical synopsis terms, may be subheadings or leaf nodes MRCONSO.TTY = "HT"
MRCONSO.TTY = "PTCS"

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

Relationships are created to connect PTCS to PT atoms:
REL = RO
RELA = manifestation_of/has_manifestation

Relationships are created to connect PTCSto PT atoms:
REL = RO
RELA = inheritance_type_of/has_inheritance_type
<Mim-entry_synopsisEditHistory><Mim-date_year> Clinical synopsis year Used to determine which clinical synopsis records to process for inclusion in the Metathesaurus.
Records added before 1996 are not processed.