Skip Navigation Bar

Unified Medical Language System® (UMLS®)

2013AB 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

Notes

Summary of Changes:

  (return to top)

No changes have been made to the original data file format or to representation of OMIM in 2013AB.

Source-Provided Files: Summary

  (return to top)

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

  (return to top)

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 = "SYN"
MRCONSO.TTY = "ACR"

Information before the first semicolon is used to create SYN atoms

Information after the semicolon is parsed to create ACR atoms

SYN atom is not created if the string already exists as an ACR atom

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

Relationships are created to connect SYN 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 PT to ET atoms:
REL = RO
RELA = related_to

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=SYN, ETAV, 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 = "PTAV"

The value of tag = "Mim-allelic-variant_name> is concatenated with information parsed after the first comma in the value of tag = "<Mim-allelic-variant_mutation><Mim-text_text>"

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

<Mim-allelic-variant_aliases_E>
Allelic variant aliases
MRCONSO.TTY = "ETAV"

If the pattern ", INCLUDED" is found in the string, it is removed and an ETAV atom is created

If the pattern ", INCLUDED" is not found in the string, a SYN atom is created.

Relationships are created to connect ETAV to PTAV atoms:
REL = RO
RELA = related_to

<Mim-allelic-variant_mutation><Mim_text_text>
The type of mutations which show statistical correlation to the particular disorders.
MRCONSO.TTY = "PTAV"
MRCONSO.TTY = "SYN"

For PTAV atoms, the value of tag = "Mim-allelic-variant_name> is concatenated with information parsed after the first comma in the value of tag = "<Mim-allelic-variant_mutation><Mim-text_text>"

Relationships are created to connect PTAV to SYN atoms:
REL = RO
RELA = alias_of/has_alias
<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:
  • The string mixed-case/lower-case.  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.