982173a412c443685c6a186f220849d16cdfdfde
max
  Thu Jan 30 13:44:29 2020 -0800
adding data access section to masterming, adding link to API to clinvar, no redmine, off-list email from Robert Shore

diff --git src/hg/makeDb/trackDb/human/mastermind.html src/hg/makeDb/trackDb/human/mastermind.html
index 5769e0e..3a8023e 100644
--- src/hg/makeDb/trackDb/human/mastermind.html
+++ src/hg/makeDb/trackDb/human/mastermind.html
@@ -64,30 +64,50 @@
 </table>
 </p>
 
 <p>
 The three numbers that are shown on the mouse-over and the details page have the following meaning (MM=Mastermind):
 <ul>
     <li><b>MMCNT1</b>: cDNA-level exact matches. This is the number of articles that mention the variant at the nucleotide level in either the title/abstract or the full-text.
     <li><b>MMCNT2</b>: cDNA-level possible matches. This is the number of articles with nucleotide-level matches (from 1) plus articles with protein-level matches in which the publication did not specify the cDNA-level change, meaning they could be referring to this nucleotide-level variant but there is insufficient data in these articles to determine conclusively.
     <li><b>MMCNT3</b>: This is the number of articles citing any variant resulting in the same biological effect as this variant. This includes the articles from MMCNT1 and MMCNT2 plus articles with alternative cDNA-level variants that result in the same protein effect.
 </ul>
 On the track settings page one can filter on these scores under the display mode section by entering
 a minimum number of articles for each kind of evidence.
 
 </p>
 
+<H2>Data access</H2>
+<p>
+The raw data can be explored interactively with the <a href="../cgi-bin/hgTables">Table Browser</a>
+or the <a href="../cgi-bin/hgIntegrator">Data Integrator</a>. The data can be accessed from scripts through our 
+<a href="https://api.genome.ucsc.edu">API</a>, the track name is "mastermind".
+
+<p>
+For automated download and analysis, the genome annotation is stored in a bigBed file that
+can be downloaded from
+<a href="http://hgdownload.soe.ucsc.edu/gbdb/$db/bbi/" target="_blank">our download server</a>.
+The file for this track is called <tt>mastermind.bb</tt>. Individual
+regions or the whole genome annotation can be obtained using our tool <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 tool
+can also be used to obtain only features within a given range, e.g. 
+<tt>bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg19/bbi/mastermind.bb -chrom=chr21 -start=0 -end=100000000 stdout</tt></p>
+</p>
+
 <h2>Methods</h2>
 
 <p>The Mastermind Cited Variants file was <a target=_blank href="https://www.genomenon.com/cvr/">downloaded</a>,
 converted to BED format with scripts that are available in our 
 <a target=_blank href="https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/utils/otto/mastermind">Git
 repository</a> and converted to a bigBed file with the UCSC genome browser tool
 bedToBigBed.</p>
 
 <p>This track is automatically updated two weeks after every Mastermind CVR release, which happens every three months.</p>
 
 
 <h2>Credits</h2>
 
 <p>
 Thanks to Mark Kiel, Steve Schwartz and Clayton Wheeler from Genomenon for making these data available.