This page lists UMLS Metathesaurus data elements and traces them back to the specific source data that populates them.
VSAB: OMIM2023_02_05
No changes were made to the OMIM source format. In the Metathesaurus, relationships (RQ/entry_term_of) were added between PTs and their ETs.
XML records are formatted to Metathesaurus specifications.
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:
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> Parenthetical frequency information such as "1 family" or "1 patient" may be removed from the atom name and is included as an attribute on the relationship to the preferred form. See ATN = "QUALIFIER" 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 Parenthetical frequency information such as "1 family" or "1 patient" may be removed from the atom name and is included as an attribute on the relationship to the preferred form. See ATN = "QUALIFIER" 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 Parenthetical frequency information such as "In some patients" or "rare" may be removed from the atom name and is included as an attribute on the relationship to the preferred form. See ATN = "QUALIFIER" SDUI: An MTHU# assigned during Metathesaurus source processing |
Attribute Name | Origin |
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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. |
QUALIFIER | Parenthetical information indicating frequency, stripped from the PTCS, PHENO, or PHENO_ET string in the original source data. Examples include "In some patients," "rare," or "1 family." STYPE = RUI. |
SOS | Strings in the "MISCELLANEOUS" and "MOLECULAR BASIS" branches of the Clinical Synopsis (PTCS tree). STYPE = AUI. |
REL | RELA Inverse RELA |
ORIGIN |
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PAR CHD |
(no rela) | Hierarchy representing the clinical synopses. All atoms with TTY = HT or PTCS participate in the hierarchy. |
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 | phenotype_of has_phenotype |
Connects PTAV to PHENO or PHENO_ET |
RQ | alias_of has_alias |
Connects ETAL atom to PT atom |
RQ | allelic_variant_of has_allelic_variant |
Connects PTAV atom to its PT atom |
RQ | entry_term_of has_entry_term |
Connects PT atom to its ET atoms |
SY | expanded_form has_expanded_form |
Connects ACR atom to ET, ETAL or PT atom |