90df56c8f9c941333d27c86fc8c81063734cdf4f lrnassar Tue Jan 25 11:58:59 2022 -0800 Adding section describing how to get UCSC format files from OMIM. Refs Max diff --git src/hg/makeDb/trackDb/human/omimLocation.html src/hg/makeDb/trackDb/human/omimLocation.html index 6fc1f93..8de8898 100644 --- src/hg/makeDb/trackDb/human/omimLocation.html +++ src/hg/makeDb/trackDb/human/omimLocation.html @@ -39,30 +39,59 @@ This track was constructed as follows:

The data file genemap.txt from OMIM was loaded into the MySQL table omimGeneMap.
Entries in genemap.txt having disorder info were parsed and loaded into the omimPhenotype table. The phenotype map keys (the numbers (1)(2)(3)(4) from the disorder columns) were placed into a separate field.
The cytogenetic location data (from the location column in omimGeneMap) were parsed and converted into genomic start and end positions based on the cytoBand table. These genomic positions, together with the corresponding OMIM IDs, were loaded into the omimLocation table.
All entries with no associated phenotype map key and all OMIM gene entries as reported in the "OMIM Genes" track were then excluded from the omimLocation table.

Data Access

+Since 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