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/omimAvSnp.html src/hg/makeDb/trackDb/human/omimAvSnp.html index 692748e..d59e44c 100644 --- src/hg/makeDb/trackDb/human/omimAvSnp.html +++ src/hg/makeDb/trackDb/human/omimAvSnp.html @@ -1,61 +1,90 @@ <H2>Description</H2> <!--#insert file="omimDescriptionText.html"--> <P> This track shows the <B>allelic variants</B> in the Online Mendelian Inheritance in Man (<A HREF="https://www.omim.org/" TARGET=_blank>OMIM</A>) database that have associated <A HREF="https://www.ncbi.nlm.nih.gov/projects/SNP/" TARGET=_blank>dbSNP</A> identifiers. </P> <H2>Display Conventions and Configuration</H2> <P>Genomic positions of OMIM allelic variants are marked by solid blocks, which appear as tick marks when zoomed out. <P> The details page for each variant displays the allelic variant description, the amino acid replacement, and the associated <a href="https://www.ncbi.nlm.nih.gov/projects/SNP/" target="_blank">dbSNP</a> and/or <a href="https://www.ncbi.nlm.nih.gov/clinvar/" target="_blank">ClinVar</a> identifiers with links to the variant's details at those resources. </P> <P>The descriptions of OMIM entries are shown on the main browser display when Full display mode is chosen. In Pack mode, the descriptions are shown when mousing over each entry. </P> <H2>Methods</H2> <P> This track was constructed as follows: <UL> <LI>The OMIM allelic variant data file <TT>mimAV.txt</TT> was obtained from OMIM and loaded into the MySQL table <TT>omimAv</TT>. <LI>The genomic position for each allelic variant in <TT>omimAv</TT> with an associated dbSnp identifier was obtained from the <TT>snp151</TT> table. The OMIM AV identifiers and their corresponding genomic positions from dbSNP were then loaded into the <TT>omimAvSnp</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/McKusick-s-Online-Mendelian- Inheritance-in-Man" 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> <p> Hamosh A, Scott AF, Amberger JS, Bocchini CA, McKusick VA. <a href="https://academic.oup.com/nar/article/33/suppl_1/D514/2505259/Online-Mendelian-Inheritance- in-Man-OMIM-a" target="_blank"> Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders</a>. <em>Nucleic Acids Res</em>. 2005 Jan 1;33(Database issue):D514-7. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/15608251" target="_blank">15608251</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC539987/" target="_blank">PMC539987</a> </p>