This page lists specific source data elements and provides information on their representation in the UMLS Metathesaurus.
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 supplied according to Metathesaurus specifications.
| File Name | Description |
|---|---|
| http://omim.org/help/faq |
FAQ |
Not included: Data from many tags are not included in Metathesaurus source processing, because they do not contain terminological content.
The following is a list of elements available for OMIM data in XML format.
Required Elements:
| Element | Description | Representation | ||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| <Mim-entry_mimNumber> | Unique identifier | MRCONSO.CODE MRCONSO.SDUI |
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| <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.
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| <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 Relationships are created to connect PT to ET atoms: REL = RQ RELA = entry_term_of/has_entry_term |
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 Relationships are created to connect ET to PT atoms: REL = RQ RELA = entry_term_of/has_entry_term 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. In many cases, parenthetical information such as "1 family" or "1 patient" indicates frequency. This segment of the string has been stripped and is represented as an attribute connected to the PHENO - PTAV RUI. | 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. In many cases, parenthetical information such as "1 family" or "1 patient" indicates frequency. This segment of the string has been stripped and is represented as an attribute connected to the PHENO_ET - PTAV RUI. 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:
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| <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. In many cases, parenthetical information such as "in some families" or "rare" indicates frequency. This segment of the string has been stripped and is represented as an attribute connected to the PTCS - PT RUI. Values that are treed under "MISCELLANEOUS" or "MOLECULAR BASIS" are represented as attributes (ATN = SOS). 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. |