Schema for Mastermind Variants - Genomenon Mastermind Variants extracted from full text publications
  Database: hg19    Primary Table: mastermind Data last updated: 2020-10-08
Big Bed File: /gbdb/hg19/bbi/mastermind.bb
Item Count: 2,290,299
Format description: mastermind bed: bed9 + various fields
fieldexampledescription
chromchr1Chromosome (or contig, scaffold, etc.)
chromStart166810198Start position in chromosome
chromEnd166810199End position in chromosome
nameG>TName of item
score0Score from 0-1000
strand.+ or -
thickStart166810198Start of where display should be thick (start codon)
thickEnd166810199End of where display should be thick (stop codon)
reserved130,130,210Used as itemRgb as of 2004-11-22
urlhttps://mastermind.genomenon.com/detail?mutation=NC_000001.10%3Ag.166810199G%3ET&ref=ucsc|POGK:E2DProtein change and link to details
genePOGKGene symbol
mmcnt10MMCNT1 - articles with exact cDNA change
mmcnt21MMCNT2 - articles with exact cDNA and/or protein change
mmcnt31MMCNT3 - articles with same protein change
_mouseOverPOGK:E2D - 0/1/1mouse over

Sample Rows
 
chromchromStartchromEndnamescorestrandthickStartthickEndreservedurlgenemmcnt1mmcnt2mmcnt3_mouseOver
chr1166810198166810199G>T0.166810198166810199130,130,210https://mastermind.genomenon.com/detail?mutation=NC_000001.10%3Ag.166810199G%3ET&ref=ucsc|POGK:E2DPOGK011POGK:E2D - 0/1/1
chr1166810198166810199G>C0.166810198166810199130,130,210https://mastermind.genomenon.com/detail?mutation=NC_000001.10%3Ag.166810199G%3EC&ref=ucsc|POGK:E2DPOGK011POGK:E2D - 0/1/1
chr1166815852166815853C>T0.166815852166815853130,130,210https://mastermind.genomenon.com/detail?mutation=NC_000001.10%3Ag.166815853C%3ET&ref=ucsc|POGK:P46LPOGK011POGK:P46L - 0/1/1
chr1166815933166815934G>A0.166815933166815934130,130,210https://mastermind.genomenon.com/detail?mutation=NC_000001.10%3Ag.166815934G%3EA&ref=ucsc|POGK:R73QPOGK011POGK:R73Q - 0/1/1
chr1166818175166818176A>T0.166818175166818176130,130,210https://mastermind.genomenon.com/detail?mutation=NC_000001.10%3Ag.166818176A%3ET&ref=ucsc|POGK:E2DPOGK011POGK:E2D - 0/1/1
chr1166818175166818176A>C0.166818175166818176130,130,210https://mastermind.genomenon.com/detail?mutation=NC_000001.10%3Ag.166818176A%3EC&ref=ucsc|POGK:E2DPOGK011POGK:E2D - 0/1/1
chr1166818302166818303G>A0.16681830216681830350,80,160https://mastermind.genomenon.com/detail?mutation=NC_000001.10%3Ag.166818303G%3EA&ref=ucsc|POGK:E163KPOGK022POGK:E163K - 0/2/2
chr1166818309166818310G>C0.166818309166818310130,130,210https://mastermind.genomenon.com/detail?mutation=NC_000001.10%3Ag.166818310G%3EC&ref=ucsc|POGK:S165TPOGK011POGK:S165T - 0/1/1
chr1166818363166818364C>T0.166818363166818364130,130,210https://mastermind.genomenon.com/detail?mutation=NC_000001.10%3Ag.166818364C%3ET&ref=ucsc|POGK:A183VPOGK001POGK:A183V - 0/0/1
chr1166818776166818777C>T0.166818776166818777130,130,210https://mastermind.genomenon.com/detail?mutation=NC_000001.10%3Ag.166818777C%3ET&ref=ucsc|POGK:L321LPOGK011POGK:L321L - 0/1/1

Mastermind Variants (mastermind) Track Description
 

Description

This track shows most variants found in the full text of scientific publications gathered by Genomenon Mastermind. Mastermind uses a software that searches for disease-gene-variant associations in the scientific literature. The genome browser track shows only if a variant has been indexed by the search engine.

To get details on a variant (bibliographic references, disease, etc) click it and follow the "Protein change and link to details" at the top of the details page. Mouse over an item to show the gene and amino acid change and the scores MMCNT1, MMCNT2 and MMCNT3, explained below.

Genomenon Mastermind Genomic Search Engine is a commercial database of variants likely to be mentioned in full text scientific articles. A limited number of queries per week is free for healthcare professionals and researchers, if they register on the signup page page. Advanced features require a license for the Mastermind Professional Edition, which contains the same content but allows more comprehensive searches.

Display Conventions and Configuration

Genomic locations of variants are labeled with the nucleotide change. Hover over the features to see the gene, the amino acid change and the scores MMCNT1, MMCNT2 and MMCNT3, described below. All other information is shown on the respective Mastermind variant detail page, accessible via the "Protein change and link to details" at the top of the details page. The features are colored based on their evidence:

As suggested by Genomenom, we added a filter on all variants, so the data are not exactly identical to their website. We skip variants with more than one nucleotide and a MMCNT of 0 and where the variant is not an indel. This means that for longer variants, only variants are shown that are explicitly mentioned in the papers. This makes the data more specific.

Color Level 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

The three numbers that are shown on the mouse-over and the details page have the following meaning (MM=Mastermind):

  • MMCNT1: 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.
  • MMCNT2: 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.
  • MMCNT3: 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.
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.

Data access

The raw data can be explored interactively with the Table Browser or the Data Integrator. The data can be accessed from scripts through our API, the track name is "mastermind".

For automated download and analysis, the genome annotation is stored in a bigBed file that can be downloaded from our download server. The file for this track is called mastermind.bb. Individual regions or the whole genome annotation can be obtained using our tool bigBedToBed 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 here. The tool can also be used to obtain only features within a given range, e.g. bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg19/bbi/mastermind.bb -chrom=chr21 -start=0 -end=100000000 stdout

Methods

The Mastermind Cited Variants file was downloaded, converted to BED format with scripts that are available in our Git repository and converted to a bigBed file with the UCSC genome browser tool bedToBigBed.

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

Credits

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