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 <TT>omimGene2</tt> table, the primary table for this track. </P> </UL> <P> *The locations in the <TT>refGene</TT> table are from alignments of RefSeq Genes to the reference genome using BLAT. </P> <h2>Data Access</h2> <p> 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 <a href="https://omim.org/downloads/" target="_blank">OMIM Downloads page</a>. All genome-wide downloads are freely available from OMIM after registration.</p> <p> +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 +<a href="https://omim.org/contact" target="_blank">https://omim.org/contact</a>. 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.</p> +<p> UCSC offers queries within chromosomes from <a href="hgTables" target=_blank>Table Browser</a> that include a variety of filtering options and cross-referencing other datasets using our <a href="hgIntegrator" target=_blank>Data Integrator</a> tool. UCSC also has an <a href="../goldenPath/help/api.html" target=_blank>API</a> that can be used to retrieve data in JSON format from a particular chromosome range.</p> - -<p>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 -<a href="https://omim.org/contact">https://omim.org/contact</a>. 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.</p> - <p> Please refer to our searchable <A HREF="https://groups.google.com/a/soe.ucsc.edu/forum/?hl=en&fromgroups#!search/download+snps" target=_blank>mailing list archives</a> for more questions and example queries, or our <a HREF="../FAQ/FAQdownloads.html#download36" target=_blank>Data Access FAQ</a> for more information.</p> <h4>Example: Retrieve phenotype, Mode of Inheritance, and other OMIM data within a range</h4> <ol> <li>Go to <a href="hgTables">Table Browser</a>, make sure the right dataset is selected: group: Phenotype and Literature, track: OMIM Genes, table: <tt>omimGene2</tt>.</li> <li>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.</li> <li>Format your data by setting the "Output format" dropdown to "selected fields from primary