SoyMine: Home

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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.

Click here to see the US Germplasm genotyping study, added in v0.10. Let us know how you'd like us to improve the genotype matrix viewer!

v0.10 (April, 2019)

Organisms are now a genus+species (or NCBI taxon ID); a new entity Strains distinguishes specific lines/genomes/etc. Every SequenceFeature is associated with a Strain.
We've switched to Apache Solr search, which is significantly faster.

Genomic queries, leading to genes and other chromosome features. Read more

Query for genomics:

Queries on homology, synteny, etc. Read more

Query for comparison:

Queries on GO terms, etc. Read more

Query for function:

GO Term Genes
GO Term Genes + Upstream Flanking Regions
Gene Description Proteins
Gene Ontology Terms
Gene description Genes

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

Query for expression:

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

Query for genetics:

Phenotype GWAS

Queries resulting in publication lists. Read more

Query for publications:

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:

The Legume Information System (LIS) is a research project of the
USDA-ARS:Corn Insects and Crop Genetics Research in Ames, IA.

Mine development is also supported by the Legume Federation,
an NSF project to federate legume resources around the world.

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