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/omimGene2.html src/hg/makeDb/trackDb/human/omimGene2.html index c4086cc..df13603 100644 --- src/hg/makeDb/trackDb/human/omimGene2.html +++ src/hg/makeDb/trackDb/human/omimGene2.html @@ -132,45 +132,44 @@ 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 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.

- -

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.

-

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

  1. Go to Table Browser, make sure the right dataset is selected: group: Phenotype and Literature, track: OMIM Genes, table: omimGene2.
  2. 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.
  3. Format your data by setting the "Output format" dropdown to "selected fields from primary