Unified Medical Language System® (UMLS®)
2012AB Online Mendelian Inheritance in Man Source Information
Notes
Summary of Changes:
)No changes have been made to the original data file format or
to representation of OMIM in 2012AB.
Source-Provided Files: Summary
()XML records are downloaded and formatted to Metathesaurus
specifications.
Documentation and Reference
| File Name | Description |
|---|---|
| http://www.ncbi.nlm.nih.gov/dtd/NCBI_Mim.mod.dtd | XML dtd |
| http://www.ncbi.nlm.nih.gov/Omim/omimfaq.html |
FAQ |
XML Data
Not included: <Mim-entry_copyright>, <Mim-entry_seeAlso>, <Mim-entry_text>, <Mim-entry_textfields>, <Mim-entry_hasSummary>, <Mim-entry_summary>, <Mim-entry_summaryAttribution>, <Mim-entry_summaryEditHistory>, <Mim-entry_summaryCreationDate, <Mim-entry_hasSynopsis>, <Mim-entry_synopsisCreationDate>, <Mim-entry_editHistory>, <Mim-entry_creationDate>, <Mim-entry_references>, <Mim-entry_attribution>,<Mim-entry_numGeneMaps>, <Mim-entry_medlineLinks>, <Mim-entry_proteinLinks>, <Mim-entry_nucleotideLinks>, <Mim-entry_structureLinks>, <Mim-entry_genomeLinks>
Source-Provided Data: Details
()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.
|
||||||||||||||||||
| <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. |
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 |
| <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 |
| <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>" |
| <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 |
| <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>" |
| <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:
|
| <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 |
| <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. |
