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Unified Medical Language System® (UMLS®)

2012AB Online Mendelian Inheritance in Man Source Information




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

VSAB: OMIM_2012_05_02

Summary of Changes

No changes have been made to the format of original data files or to UMLS source processing.

Source Provided Files:

XML records are downloaded and 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:
    • For termtypes ACR, ET, PT: <Mim-entry_mimNumber>
    • For termtype SYN:
      • For tag <Mim-entry_aliases_E>:  <Mim-entry_mimNumber>
      • For tags <Mim-allelic-variant_aliases_E> and <Mim-allelic-variant_mutaion>:  <Mim-entry_mimNumber>.<Mim-allelic-variant_number>
    • For termtypes ETAV, PTAV: <Mim-entry_mimNumber>.<Mim-allelic-variant_number> (e.g. "606158.0015")
    • For termtypes HT, PTCS:  an MTHU# assigned during Metathesaurus source processing
  • SAUI:  not applicable
  • SCUI:  not applicable
  • SDUI:  same as CODE

Atoms (MRCONSO):

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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>
ETAV
CODE: <Mim-entry_mimNumber>.<Mim-allelic-variant_number>

STRING:
value of tag = <Mim-allelic-variant_aliases_E>
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

SDUI:  <Mim-entry_mimNumber>.<Mim-allelic-variant_number>
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
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_name> concatenated with information after the first comma from 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

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
SYN
CODE:
For tag <Mim-entry_aliases_E>:  <Mim-entry_mimNumber>
For tags <Mim-allelic-variant_aliases_E> and <Mim-allelic-variant_mutaion>:  <Mim-entry_mimNumber>.<Mim-allelic-variant_number>

STRING:
value of tag = <Mim-entry_aliases_E>
Information before the semicolon is used to create a SYN atom
SYN atom is not created if the string already exists as an ACR atom

value of tag = <Mim-allelic-variant_aliases_E>
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

value of tag = <Mim-allelic-variant_mutation><Mim-text_text>

SDUI: <Mim-entry_mimNumber>

Attributes (MRSAT):

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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):

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No definitions are included in the OMIM data.


Relationships (MRREL):

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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
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
RO
related_to
Connects ET atom to PT atom
Connects ETAV atom to PTAV atom
RQ
alias_of
has_alias
Connects SYN atom to PT or PTAV atom
SY
expanded_form
has_expanded_form
Connects ACR atom to ET, PT or SYN atom

Mappings (MRMAP):

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No mappings to external sources are processed from OMIM data.