bbd718a03c8042b1ff26617d7dd2964463e745f4 dschmelt Fri Oct 21 10:43:48 2022 -0700 Final tdb changes for hgnc and panelapp refs #30097, #29891 diff --git src/hg/makeDb/trackDb/human/hgnc.html src/hg/makeDb/trackDb/human/hgnc.html index a90d2d1..702a358 100644 --- src/hg/makeDb/trackDb/human/hgnc.html +++ src/hg/makeDb/trackDb/human/hgnc.html @@ -1,20 +1,31 @@ <h2>Description</h2> <p> -The <a href="https://www.genenames.org/tools/search" target="_blank">HGNC</a> is responsible for approving unique symbols and names for human loci, including protein coding genes, ncRNA genes and pseudogenes, to allow unambiguous scientific communication. +The <a href="https://www.genenames.org/tools/search" target="_blank">HGNC</a> is +responsible for approving unique symbols and names for human loci, including protein +coding genes, ncRNA genes and pseudogenes, to allow unambiguous scientific communication. <p> -For each known human gene the HGNC approves a gene name and symbol (short-form abbreviation). All approved symbols are stored in the HGNC database, www.genenames.org, a curated online repository of HGNC-approved gene nomenclature, gene groups and associated resources including links to genomic, proteomic and phenotypic information. Each symbol is unique and we ensure that each gene is only given one approved gene symbol. It is necessary to provide a unique symbol for each gene so that we and others can talk about them, and this also facilitates electronic data retrieval from publications and databases. In preference each symbol maintains parallel construction in different members of a gene family and can also be used in other species, especially other vertebrates including mouse. +For each known human gene, the HGNC approves a gene name and symbol (short-form abbreviation). +All approved symbols are stored in the HGNC database, <a href="https://genenames.org" +target="_blank">www.genenames.org</a>, a curated online repository of HGNC-approved gene +nomenclature, gene groups and associated resources including links to genomic, proteomic, +and phenotypic information. Each symbol is unique and we ensure that each gene is only +given one approved gene symbol. It is necessary to provide a unique symbol for each gene +so that we and others can talk about them, and this also facilitates electronic data +retrieval from publications and databases. In preference, each symbol maintains +parallel construction in different members of a gene family and can also be +used in other species, especially other vertebrates including mouse. <h2>Data Access</h2> <p> The raw data can be explored interactively with the <a href="../cgi-bin/hgTables" target="_blank">Table Browser</a>, or the <a href="../cgi-bin/hgIntegrator" target="_blank">Data Integrator</a>. For computational analysis, genome annotations are stored in a bigBigFile file that can be downloaded from the <a href="http://hgdownload.soe.ucsc.edu/gbdb/$db/hgnc/hgnc.bb" target="_blank">download server</a>. Regional or genome-wide annotations can be converted from binary data to human readable text using our command line utility <em>bigBedToBed</em> which can be compiled from source code or downloaded as a precompiled binary for your system. Files and instructions can be found in the <a href="http://hgdownload.soe.ucsc.edu/admin/exe/" target="_blank">utilities directory</a>. The utility can be used to obtain features within a given range, for example:</p> <code>bigBedToBed -chrom=chr6 -start=0 -end=1000000 http://hgdownload.soe.ucsc.edu/gbdb/hg38/hgnc/hgnc.bb stdout</code>