cfe373a8c5d27a4cdac6ce39b2a50f5cf4e63948 dschmelt Fri Jul 31 14:11:36 2020 -0700 Adding Data Access and example for OMIM refs #18419 diff --git src/hg/makeDb/trackDb/human/omimGene2.html src/hg/makeDb/trackDb/human/omimGene2.html index d87b41d..9078352 100644 --- src/hg/makeDb/trackDb/human/omimGene2.html +++ src/hg/makeDb/trackDb/human/omimGene2.html @@ -125,30 +125,73 @@ <LI>Entries in <TT>genemap.txt</TT> having disorder info were parsed and loaded into the <TT>omimPhenotype</TT> table. <LI>For each OMIM gene in the <TT>omim2gene</TT> table, the <A HREF="https://www.ncbi.nlm.nih.gov/gene" TARGET=_blank>Entrez Gene ID</A> was used to get the corresponding <a href="https://www.ncbi.nlm.nih.gov/refseq/" target="_blank">RefSeq Gene ID</a> via the <TT>refLink</TT> table, and the RefSeq ID was used to get the genomic location from the <TT>refGene</TT> table.* The OMIM gene IDs and corresponding RefSeq Gene locations were loaded into 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> +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> + +<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 following options are selected: +group: Phenotype and Literature, track: OMIM Genes, table: <tt>omimGene2</tt>.</li> +<li>Enter coordinates or a gene symbol into the "Position" textbox, such as +chr1:11,106,535-11,262,551 or MTOR.</li> +<li>Change the "Output format" dropdown to "selected fields from primary +and related Tables" and click <button>get output</button>. Instead of returning +the standard formatted dataset from the <tt>omimGene2</tt> table, this +bring up the data field and linked table selection page.</li> +<li>Select chrom, chromStart, chromEnd,and name from omimGene2 table. Then select the related tables <tt>omim2gene</tt> +and <tt>omimPhenotype</tt> and click <button>allow selection from check tables</button>. +This brings up the fields of the linked tables, where you can select approvedGeneSymbol, +omimID, description, omimPhenotypeMapKey, and inhMode. </li> +<li>Click on the <button>get output</button> will bring you to the results page: +<pre>chr1 11166591 11322608 MTOR 601231, Smith-Kingsmore syndrome,Focal cortical dysplasia, type II, somatic, 3, Autosomal dominant</pre></li></ol> +<p>For a quick link to pre-fill these options, click +<a href="http://genome.ucsc.edu/cgi-bin/hgTables?hgS_doOtherUser=submit&hgS_otherUserName=dschmelt&hgS_otherUserSessionName=omimPhenotypeTableBrowserEx19"> +this session link</a>. + + <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>