bcfd0204545186c59bf40fa9472014aab0cf16f6 dschmelt Fri Jul 31 16:45:19 2020 -0700 Slight modifications for omim Data Access #18419 diff --git src/hg/makeDb/trackDb/human/omimGene2.html src/hg/makeDb/trackDb/human/omimGene2.html index e9bb83e..203a6c5 100644 --- src/hg/makeDb/trackDb/human/omimGene2.html +++ src/hg/makeDb/trackDb/human/omimGene2.html @@ -149,43 +149,42 @@ 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: +<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>Enter coordinates or a gene symbol into the "Position" textbox, such as -chr1:11,166,591-11,322,608 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>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 +and related Tables" and click <button>get output</button>. This +brings 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: +<li>Click on the <button>get output</button> to proceed 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">