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: <UL> <LI>The data file <TT>genemap.txt</TT> from OMIM was loaded into the MySQL table <TT>omimGeneMap</TT>. <LI>Entries in <TT>genemap.txt</TT> having disorder info were parsed and loaded into the <TT>omimPhenotype</TT> table. The phenotype map keys (the numbers (1)(2)(3)(4) from the disorder columns) were placed into a separate field. <LI>The cytogenetic location data (from the location column in <TT>omimGeneMap</TT>) were parsed and converted into genomic start and end positions based on the <TT>cytoBand</TT> table. These genomic positions, together with the corresponding OMIM IDs, were loaded into the <TT>omimLocation</TT> table. <LI>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 <TT>omimLocation</TT> table. </UL> +<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> +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> + <H2>Credits</H2> <P> 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.</P> <H2>References</H2> <p> Amberger J, Bocchini CA, Scott AF, Hamosh A. <a href="https://academic.oup.com/nar/article/37/suppl_1/D793/1003813" target="_blank"> McKusick's Online Mendelian Inheritance in Man (OMIM)</a>. <em>Nucleic Acids Res</em>. 2009 Jan;37(Database issue):D793-6. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/18842627" target="_blank">18842627</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686440/" target="_blank">PMC2686440</a> </p>