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Search this mine. Enter names, identifiers or keywords. Examples: Glyma.01G086900, Glyma.01G086900.1, BARCSOYSSR_04_1400, Seed yield 15-5, R-GMA-8879007.1, David Grant.

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Welcome to the LIS SoyMine!

This mine integrates many types of data for soybean. It is currently under development by LIS, built from the LIS chado database (genomic data) and the SoyBase database (genetic data) as well as some flat files. Contact Sam Hokin shokin at ncgr dot org.

Latest updates (v0.10, October 2018)

  • We've added the big BARC_1059007 genotyping study, which genotyped all of the GRIN soybean accessions using the SoySNP50K BeadChip.
  • To support the above, we've imported the GRIN soybean lines (as GenotypingLine) along with their Phenotype information.
  • New displayer: a genotyping matrix viewer for the genotyping study
  • New displayer: an allele counter on genetic marker report pages
  • New displayer: a scatterplot of QTL p-values on GWAS experiments (think Manhattan plot)
A note about "Organism"
InterMine associates an "Organism" with a distinct genome. Therefore, you will find many soybean "organisms" in this mine, which represent different varieties. However, some quantities, like genetic markers, are not associated with a specific variety; in that case, they are associated with and placed on the reference Williams82 genome.

Queries on homology, synteny, etc. Read more


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Queries on gene expression, resulting in gene lists. Read more


Query for expression:

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Queries on genetic data: QTLs, genetic maps, markers, etc. Read more


Query for genetics:

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Queries resulting in publication lists. Read more


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Perl, Python, Ruby and Java API

perl java python ruby

Access our SoyMine data via our Application Programming Interface (API) too! We provide client libraries in the following languages: