e55d5d49dfead30ba3c279307ed460f25d729d0a gperez2 Fri May 24 14:48:39 2024 -0700 Fixing broken links, No redmine diff --git src/hg/makeDb/trackDb/human/omimAvSnp.html src/hg/makeDb/trackDb/human/omimAvSnp.html index 2590246..f37fcd6 100644 --- src/hg/makeDb/trackDb/human/omimAvSnp.html +++ src/hg/makeDb/trackDb/human/omimAvSnp.html @@ -1,94 +1,94 @@

Description

This track shows the allelic variants in the Online Mendelian Inheritance in Man (OMIM) database that have associated -dbSNP identifiers. +dbSNP identifiers.

Display Conventions and Configuration

Genomic positions of OMIM allelic variants are marked by solid blocks, which appear as tick marks when zoomed out.

The details page for each variant displays the allelic variant description, the amino acid replacement, and the associated -dbSNP and/or +dbSNP and/or ClinVar identifiers with links to the variant's details at those resources.

The descriptions of OMIM entries are shown on the main browser display when Full display mode is chosen. In Pack mode, the descriptions are shown when mousing over each entry.

Methods

This track was constructed as follows:

The OMIM allelic variant data file mimAV.txt was obtained from OMIM and loaded into the MySQL table omimAv.
The genomic position for each allelic variant in omimAv with an associated dbSnp identifier was obtained from the snp151 table. The OMIM AV identifiers and their corresponding genomic positions from dbSNP were then loaded into the omimAvSnp table.

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.

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