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

Description

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\nThis track shows most variants found in the full text of scientific publications gathered by\nGenomenon Mastermind. 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

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\nTo get details on a variant (bibliographic references, disease, etc)\nclick it and follow the "Protein change and link to details" 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

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\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\nsignup\npage page. Advanced features require a license for the\nMastermind Professional Edition, \nwhich contains the same content but allows more comprehensive searches.\n

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Display Conventions and Configuration

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\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 "Protein change and link to details" at the top of the details page. The\nfeatures are colored based on their evidence:\n

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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

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\n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n
ColorLevel of support
High: at least one paper mentions this exact cDNA change
Medium: at least two paper mention a variant that leads to the same amino acid change
Low: only a single paper mentions a variant that leads to the same amino acid change
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\nThe three numbers that are shown on the mouse-over and the details page have the following meaning (MM=Mastermind):\n

\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

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Methods

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The Mastermind Cited Variants file was downloaded,\nconverted to BED format with scripts that are available in our \nGit\nrepository and converted to a bigBed file with the UCSC genome browser tool\nbedToBigBed.

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This track is automatically updated two weeks after every Mastermind CVR release, which happens every three months.

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Credits

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\nThanks to Mark Kiel, Steve Schwartz and Clayton Wheeler from Genomenon for making these data available.\n

\n\n\n\n phenDis 1 bigDataUrl /gbdb/hg19/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