Unified Medical Language System® (UMLS®)
2012AB Online Mendelian Inheritance in Man Source Information
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):
)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 |
| 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:
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
|
| 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
|
| 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):
)| 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. |
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 |
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):
)No mappings to external sources are processed from OMIM
data.
