2596c3765d9f8fb8ffe464d7d11ba843374f672a
lrnassar
  Wed Feb 12 12:49:11 2025 -0800
MITOMAP track is now ready for QA, refs #24849

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+<h2>Description</h2>
+
+<p>
+This track shows annotations from <a target="_blank"
+href="https://www.mitomap.org/foswiki/bin/view/MITOMAP/WebHome">MITOMAP</a>.
+MITOMAP is a database of human mitochondrial DNA (mtDNA) information containing
+a compilation of mtDNA variation. It allows users to look up human mitochondrial gene 
+loci, search for public mitochondrial sequences, and browse or search for reported 
+general population nucleotide variants as well as those reported in clinical disease.
+</p>
+
+<h2>Display Conventions and Configuration</h2>
+<p>
+These data are separated into two tracks:<br><br>
+<b>MITOMAP Control and Coding Variants</b><br><br>
+This data track contains variants, including mini insertions and deletions, in the
+complete mtDNA. The item colors correspond to the variant type:
+<b><font color="#53AF01">control region</font></b> vs.
+<b><font color="#3E89D3">coding region</font></b>.</p>
+<p>
+<b>MITOMAP Disease Mutations</b><br><br>
+This data track contains disease-annotated mutations (variants) in the
+complete mtDNA. The item colors correspond to the variant type:
+<b><font color="##015587">coding/control</font></b> vs.
+<b><font color="#9933FF">rRNA/tRNA</font></b>.</p>
+<p>
+For both tracks, item names correspond to the
+variant nucleotide change, and mousing over features displays all available
+metadata for MITOMAP. Linkouts to the specific MITOMAP datasets are available from
+the item description pages, however, you must input the variant on MITOMAP.</p>
+
+<h2>Data Access</h2>
+<p>
+All source data can be found on the <a target="_blank" href="https://www.mitomap.org/foswiki/bin/view/MITOMAP/WebHome">
+MITOMAP site</a>.
+<p>
+The MITOMAP data on the UCSC Genome Browser can be explored interactively with the
+<a href="../cgi-bin/hgTables">Table Browser</a> or the
+<a href="../cgi-bin/hgIntegrator">Data Integrator</a>.
+For automated download and analysis, the genome annotation is stored at UCSC in bigBed
+files that can be downloaded from the respective file, e.g. 
+<a href="http://hgdownload.soe.ucsc.edu/gbdb/$db/bbi/mitoMapVars.bb" 
+target="_blank">MITOMAP Variants</a>, on our download server.
+The data may also be explored interactively using our
+<a href="../goldenPath/help/api.html" target="_blank">REST API</a>.</p>
+
+<p>
+The file for this track may also be locally explored using our tools <tt>bigBedToBed</tt> 
+which can be compiled from the source code or downloaded as a precompiled
+binary for your system. Instructions for downloading source code and binaries can be found
+<a href="http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads">here</a>.
+The tools can also be used to obtain features confined to a given range, e.g.,
+<br><br>
+<tt>bigBedToBed -chrom=chr1 -start=100000 -end=100500 http://hgdownload.soe.ucsc.edu/gbdb/$db/bbi/mitoMapVars.bb stdout</tt></p>
+
+<h2>Methods</h2>
+<p>
+The data were downloaded from the <a target="_blank" href="https://www.mitomap.org/foswiki/bin/view/MITOMAP/WebHome">
+MITOMAP resource</a>. For the <b>Control and Coding Variants track</b>, the following
+datasets were combined:
+<ul>
+<li><a target="_blank" href="https://www.mitomap.org/foswiki/bin/view/MITOMAP/VariantsControl">
+Control Region Variants (16024-576)</a></li>
+<li><a target="_blank" href="https://www.mitomap.org/foswiki/bin/view/MITOMAP/VariantsCoding">
+Coding & RNA Variants (577-16023, MTTF-MTTP)</a></li></ul>
+And for the <b>Disease Mutations track</b>, the following two were combined:
+<ul>
+<li><a target="_blank" href="https://www.mitomap.org/foswiki/bin/view/MITOMAP/MutationsRNA">
+rRNA/tRNA Mutations, all</a></li>
+<li><a target="_blank" href="https://www.mitomap.org/foswiki/bin/view/MITOMAP/MutationsCodingControl">
+Coding & Non-Coding/Control Region Mutations, all</a></li></ul></p>
+<p>
+<p>
+For all the details on how the data were processed and combined, see
+the <a target="_blank"
+href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/hg38/mitoMap.txt">
+MITOMAP makedoc</a>.
+</p>
+
+<h2>Credits</h2>
+<p>
+Thanks to the <a target="_blank" href="https://www.mitomap.org/foswiki/bin/view/MITOMAP/WebHome">MITOMAP resource</a> 
+for making these annotations available.</p>
+
+<h2>References</h2>
+<p>
+MITOMAP: A Human Mitochondrial Genome Database. http://www.mitomap.org, 2023
+</p>
+<p>
+Lott, M.T., Leipzig, J.N., Derbeneva, O., Xie, H.M., Chalkia, D., Sarmady, M., Procaccio, V., 
+and Wallace, D.C. 2013. mtDNA variation and analysis using MITOMAP and MITOMASTER. Current 
+Protocols in Bioinformatics 1(123):1.23.1-26. PMID: <a target="_blank" 
+href="http://www.ncbi.nlm.nih.gov/pubmed?term=25489354">25489354</a> URL: <a 
+target="_blank" href="http://www.mitomap.org/">http://www.mitomap.org</a>
+</p>