tableName	shortLabel	type	longLabel	visibility	priority	colorR	colorG	colorB	altColorR	altColorG	altColorB	useScore	private	restrictCount	restrictList	url	html	grp	canPack	settings
mastermind	Mastermind Variants	bigBed 9 +	Genomenon Mastermind Variants extracted from full text publications	1	100	0	0	0	127	127	127	0	0	0			<h2>Description</h2>\n<p>\nThis track shows most variants found in the full text of scientific publications gathered by\n<a target=_blank href="https://www.genomenon.com/">Genomenon Mastermind</a>. Mastermind\nuses a software that searches for disease-gene-variant associations in the \nscientific literature. The genome browser track shows only if a\nvariant has been indexed by the search engine.\n</p>\n\n<p>\nTo get details on a variant (bibliographic references, disease, etc)\nclick it and follow the &quot;Protein change and link to details&quot; at the top\nof the details page. Mouse over an item to show the gene and amino acid change and the \nscores MMCNT1, MMCNT2 and MMCNT3, explained below.\n</p>\n\n<p>\nGenomenon Mastermind Genomic Search Engine is a commercial database of variants\nlikely to be mentioned in full text scientific articles. A limited number of\nqueries per week is free for healthcare professionals and researchers, if they register on the\n<a href="https://mastermind.genomenon.com/users/sign_up/" target=_"blank">signup\npage</a> page. Advanced features require a license for the\n<a href="https://www.genomenon.com/mastermind-pro-upgrade/" target="_blank">Mastermind Professional Edition</a>, \nwhich contains the same content but allows more comprehensive searches.\n</p>\n\n<h2>Display Conventions and Configuration</h2>\n\n<p>\nGenomic locations of variants are labeled with the nucleotide change.\nHover over the features to see the gene, the amino acid change and the scores MMCNT1, MMCNT2 and \nMMCNT3, described below. All other information is shown on the respective Mastermind variant detail\npage, accessible via the &quot;Protein change and link to details&quot; at the top of the details page. The\nfeatures are colored based on their evidence:\n</p>\n\n<p>As suggested by Genomenom, we added a filter on all variants, so the data is not exactly identical \nto their website. We skip \nvariants with more than one nucleotide and a MMCNT of 0 and where the variant is not an indel, \nmeaning that for longer variants, only variants are shown that are explicitly\nmentioned in the papers. This makes the data more specific.\n</p>\n\n<p>\n<table>\n  <thead>\n  <tr>\n    <th style="border-bottom: 2px solid #6678B1;">Color</th>\n    <th style="border-bottom: 2px solid #6678B1;">Level of support</th>\n  </tr>\n  </thead>\n  <tr>\n    <th bgcolor="#0C0C78"></th>\n    <th align="left">High: at least one paper mentions this exact cDNA change</th>\n  </tr>\n  <tr>\n    <th bgcolor="#5050A0"></th>\n    <th align="left">Medium: at least two paper mention a variant that leads to the same amino acid change</th>\n  </tr>\n  <tr>\n    <th bgcolor="#8282D2"></th>\n    <th align="left">Low: only a single paper mentions a variant that leads to the same amino acid change</th>\n  </tr>\n</table>\n</p>\n\n<p>\nThe three numbers that are shown on the mouse-over and the details page have the following meaning (MM=Mastermind):\n<ul>\n    <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.\n    <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.\n    <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.\n</ul>\nOn the track settings page one can filter on these scores under the display mode section by entering\na minimum number of articles for each kind of evidence.\n\n</p>\n\n<h2>Methods</h2>\n\n<p>The Mastermind Cited Variants file was <a target=_blank href="https://www.genomenon.com/cvr/">downloaded</a>,\nconverted to BED format with scripts that are available in our \n<a target=_blank href="https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/utils/otto/mastermind">Git\nrepository</a> and converted to a bigBed file with the UCSC genome browser tool\nbedToBigBed.</p>\n\n<p>This track is automatically updated two weeks after every Mastermind CVR release, which happens every three months.</p>\n\n\n<h2>Credits</h2>\n\n<p>\nThanks to Mark Kiel, Steve Schwartz and Clayton Wheeler from Genomenon for making these data available.\n</p>\n\n<!-- <h2>References</h2> -->\n\n	phenDis	1	bigDataUrl /gbdb/hg38/bbi/mastermind.bb\ndataVersion /gbdb/hg19/bbi/mastermindRelease.txt\nexonNumbers off\nitemRgb on\nlongLabel Genomenon Mastermind Variants extracted from full text publications\nmmcnt1Filter 0\nmmcnt2Filter 0\nmmcnt3Filter 0\nmouseOverField _mouseOver\nnoScoreFilter on\nparent varsInPubs\nshortLabel Mastermind Variants\ntrack mastermind\ntype bigBed 9 +\nurls url=https://mastermind.genomenon.com/detail?disease=all%20diseases&$$\nvisibility dense\n