c6cd0772baa4f7bcf41e4b2d3bc0b409d7e494b0 max Mon Jan 8 05:23:45 2024 -0800 adding omim update freq, refs #32826 diff --git src/hg/makeDb/trackDb/human/omimGene2.html src/hg/makeDb/trackDb/human/omimGene2.html index 3c93b9d..22e5b9d 100644 --- src/hg/makeDb/trackDb/human/omimGene2.html +++ src/hg/makeDb/trackDb/human/omimGene2.html @@ -1,212 +1,216 @@

Description

This track shows the genomic positions of all gene entries in the Online Mendelian Inheritance in Man (OMIM) database.

Display Conventions and Configuration

Genomic locations of OMIM gene entries are displayed as solid blocks. The entries are colored according to the associated OMIM phenotype map key (if any):

Lighter Green for phenotype map key 1 OMIM records - the disorder has been placed on the map based on its association with a gene, but the underlying defect is not known.
Light Green for phenotype map key 2 OMIM records - the disorder has been placed on the map by linkage; no mutation has been found.
Dark Green for phenotype map key 3 OMIM records - the molecular basis for the disorder is known; a mutation has been found in the gene.
Purple for phenotype map key 4 OMIM records - a contiguous gene deletion or duplication syndrome; multiple genes are deleted or duplicated causing the phenotype.
Light Gray for Others - no associated OMIM phenotype map key info available.

Gene symbol, phenotype, and inheritance information, when available, are displayed on the details page for an item, and links to related RefSeq Genes and UCSC Genes are given. The descriptions of the OMIM entries are shown on the main browser display when mousing over each entry.

Mode of Inheritance Abbreviation

Autosomal Dominant AD

Autosomal Recessive AR

Digenic Dominant DD

Digenic Recessive DR

Isolated Cases IC

Mitochondrial Mi

Multifactorial Mu

Pseudoautosomal Dominant PADom

Pseudoautosomal Recessive PARec

Somatic Mosaicism SomMos

Somatic Mutation SMu

X-Linked XL

X-Linked Dominant XLD

X-Linked Recessive XLR

Y-Linked YL

Mode of Inheritance	Abbreviation
Autosomal Dominant	AD
Autosomal Recessive	AR
Digenic Dominant	DD
Digenic Recessive	DR
Isolated Cases	IC
Mitochondrial	Mi
Multifactorial	Mu
Pseudoautosomal Dominant	PADom
Pseudoautosomal Recessive	PARec
Somatic Mosaicism	SomMos
Somatic Mutation	SMu
X-Linked	XL
X-Linked Dominant	XLD
X-Linked Recessive	XLR
Y-Linked	YL

Brackets, "[ ]", before the phenotype name indicate "nondiseases," mainly genetic variations that lead to apparently abnormal laboratory test values (e.g., dysalbuminemic euthyroidal hyperthyroxinemia).

Braces, "{ }", indicate mutations that contribute to susceptibility to multifactorial disorders (e.g., diabetes, asthma) or to susceptibility to infection (e.g., malaria).

Question marks, "?", indicate that the relationship between the phenotype and gene is provisional. More details about this relationship are provided in the comment field of the map and in the gene and phenotype OMIM entries.

Methods

The mappings displayed in this track are based on OMIM gene entries, their Entrez Gene IDs, and the corresponding RefSeq Gene locations:

The data file genemap.txt from OMIM was loaded into the MySQL table omimGeneMap.
The data file mim2gene.txt from OMIM was processed and loaded into the MySQL table omim2gene.
Entries in genemap.txt having disorder info were parsed and loaded into the omimPhenotype table.
For each OMIM gene in the omim2gene table, the Entrez Gene ID was used to get the corresponding RefSeq Gene ID via the refLink table, and the RefSeq ID was used to get the genomic location from the refGene table.* The OMIM gene IDs and corresponding RefSeq Gene locations were loaded into the omimGene2 table, the primary table for this track.

*The locations in the refGene table are from alignments of RefSeq Genes to the reference genome using BLAT.

Data Updates

+This track is automatically updated once a week from OMIM data. The most recent update time is shown +at the top of the track documentation page. +

Data Access

Because OMIM has only allowed Data queries within individual chromosomes, no download files are available from the Genome Browser. Full genome datasets can be downloaded directly from the OMIM Downloads page. All genome-wide downloads are freely available from OMIM after registration.

If you need the OMIM data in exactly the format of the UCSC Genome Browser, for example if you are running a UCSC Genome Browser local installation (a partial "mirror"), please create a user account on omim.org and contact OMIM via https://omim.org/contact. Send them your OMIM account name and request access to the UCSC Genome Browser "entitlement". They will then grant you access to a MySQL/MariaDB data dump that contains all UCSC Genome Browser OMIM tables.

UCSC offers queries within chromosomes from Table Browser that include a variety of filtering options and cross-referencing other datasets using our Data Integrator tool. UCSC also has an API that can be used to retrieve data in JSON format from a particular chromosome range.

Please refer to our searchable mailing list archives for more questions and example queries, or our Data Access FAQ for more information.

Example: Retrieve phenotype, Mode of Inheritance, and other OMIM data within a range

Go to Table Browser, make sure the right dataset is selected: group: Phenotype and Literature, track: OMIM Genes, table: omimGene2.
Define region of interest by entering coordinates or a gene symbol into the "Position" textbox, such as chr1:11,166,591-11,322,608 or MTOR, or upload a list.
Format your data by setting the "Output format" dropdown to "selected fields from primary and related Tables" and click . This brings up the data field and linked table selection page.
Select chrom, chromStart, chromEnd, and name from omimGene2 table. Then select the related tables omim2gene and omimPhenotype and click . This brings up the fields of the linked tables, where you can select approvedGeneSymbol, omimID, description, omimPhenotypeMapKey, and inhMode.

Click on the to proceed to the results page:

chr1	11166591	11322608    601231  Gene: MTOR, Synonyms: FRAP1, SKS, Phenotypes: Smith-Kingsmore syndrome, AD, 3; Focal cortical dysplasia, type II, somatic, 3

For a quick link to pre-fill these options, click this session link.

Credits

Thanks to OMIM and NCBI for the use of their data. This track was constructed by Fan Hsu, Robert Kuhn, and Brooke Rhead of the UCSC Genome Bioinformatics Group.

References

Amberger J, Bocchini CA, Scott AF, Hamosh A. McKusick's Online Mendelian Inheritance in Man (OMIM). Nucleic Acids Res. 2009 Jan;37(Database issue):D793-6. PMID: 18842627; PMC: PMC2686440

Hamosh A, Scott AF, Amberger JS, Bocchini CA, McKusick VA. Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D514-7. PMID: 15608251; PMC: PMC539987