Data Sources and their Data Sets

CATHGENE3D
CDD
GO
The Gene Ontology (GO) knowledgebase is the world's largest source of information on the functions of genes. This knowledge is both human-readable and machine-readable, and is a foundation for computational analysis of large-scale molecular biology and genetics experiments in biomedical research.
GO
LINK
HAMAP
InterMine post-processor
Gene-flanking regions created by the core InterMine post-processor
InterMine gene-flanking regions
LINK
Intergenic regions created by the InterMine core post-processor
InterMine intergenic regions
LINK
InterPro
InterPro provides functional analysis of proteins by classifying them into families and predicting domains and important sites.
InterPro data set
Mapping of GO terms to InterPro entries.
InterPro domain GO annotations
LIS Datastore
CDS models for the glyma.Lee.gnm1 genome
glyma.Lee.gnm1.ann1.6NZV.cds_primaryTranscript.fna
LINK
CDS models for the glyma.Wm82.gnm1 genome
glyma.Wm82.gnm1.ann1.DvBy.cds_primaryTranscript.fna
LINK
CDS models for the glyma.Wm82.gnm2 genome
glyma.Wm82.gnm2.ann1.RVB6.cds_primaryTranscript.fna
LINK
CDS models for the glyma.Wm82.gnm4 genome
glyma.Wm82.gnm4.ann1.T8TQ.cds_primaryTranscript.fna
LINK
CDS models for the glyma.Zh13.gnm1 genome
glyma.Zh13.gnm1.ann1.8VV3.cds_primaryTranscript.fna
LINK
CDS models for the glyso.PI483463.gnm1 genome
glyso.PI483463.gnm1.ann1.3Q3Q.cds_primaryTranscript.fna
LINK
CDS models for the glyso.W05.gnm1 genome
glyso.W05.gnm1.ann1.T47J.cds_primaryTranscript.fna
LINK
Gene family assignments for glyma.Lee.gnm1 genes and proteins.
glyma.Lee.gnm1.ann1.6NZV.legfed_v1_0.M65K.gfa.tsv
LINK
Gene family assignments for glyma.Wm82.gnm1 genes and proteins.
glyma.Wm82.gnm1.ann1.DvBy.legfed_v1_0.M65K.gfa.tsv
LINK
Gene family assignments for glyma.Wm82.gnm2 genes and proteins.
glyma.Wm82.gnm2.ann1.RVB6.legfed_v1_0.M65K.gfa.tsv
LINK
Gene family assignments for glyma.Wm82.gnm4 genes and proteins.
glyma.Wm82.gnm4.ann1.T8TQ.legfed_v1_0.M65K.gfa.tsv
LINK
Gene family assignments for glyma.Zh13.gnm1 genes and proteins.
glyma.Zh13.gnm1.ann1.8VV3.legfed_v1_0.M65K.gfa.tsv
LINK
Gene family assignments for glyso.PI483463.gnm1 genes and proteins.
glyso.PI483463.gnm1.ann1.3Q3Q.legfed_v1_0.M65K.gfa.tsv
LINK
Gene family assignments for glyso.W05.gnm1 genes and proteins.
glyso.W05.gnm1.ann1.T47J.legfed_v1_0.M65K.gfa.tsv
LINK
Gene model annotation for the glyma.Lee.gnm1 genome
glyma.Lee.gnm1.ann1.6NZV.gene_models_main.gff3
LINK
Gene model annotation for the glyma.Wm82.gnm1 genome
glyma.Wm82.gnm1.ann1.DvBy.gene_models_main.gff3
LINK
Gene model annotation for the glyma.Wm82.gnm2 genome
glyma.Wm82.gnm2.ann1.RVB6.gene_models_main.gff3
LINK
Gene model annotation for the glyma.Wm82.gnm4 genome
glyma.Wm82.gnm4.ann1.T8TQ.gene_models_main.gff3
LINK
Gene model annotation for the glyma.Zh13.gnm1 genome
glyma.Zh13.gnm1.ann1.8VV3.gene_models_main.gff3
LINK
Gene model annotation for the glyso.PI483463.gnm1 genome
glyso.PI483463.gnm1.ann1.3Q3Q.gene_models_main.gff3
LINK
Gene model annotation for the glyso.W05.gnm1 genome
glyso.W05.gnm1.ann1.T47J.gene_models_main.gff3
LINK
Genetic marker positions on the glyma.Wm82.gnm2 genome assembly
glyma.Wm82.gnm2.mrk.XJP2.gff3
LINK
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.KGK20170707-1.gwas.tsv
LINK
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.KGK20170707-1.phen.tsv
LINK
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.KGK20170711-1.gwas.tsv
LINK
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.KGK20170711-1.phen.tsv
LINK
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.KGK20170714-1.gwas.tsv
LINK
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.KGK20170714-1.phen.tsv
LINK
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.KGK20170803-1.gwas.tsv
LINK
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.KGK20170803-1.phen.tsv
LINK
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.KGK20170808-1.gwas.tsv
LINK
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.KGK20170808-1.phen.tsv
LINK
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.KGK20170814-1.gwas.tsv
LINK
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.KGK20170814-1.phen.tsv
LINK
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.KGK20170908-1.gwas.tsv
LINK
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.KGK20170908-1.phen.tsv
LINK
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.KGK20170915-1.gwas.tsv
LINK
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.KGK20170915-1.phen.tsv
LINK
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.KGK20171006-1.gwas.tsv
LINK
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.KGK20171006-1.phen.tsv
LINK
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.KGK20171018-1.gwas.tsv
LINK
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.KGK20171018-1.phen.tsv
LINK
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.KGK20171027-1.gwas.tsv
LINK
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.KGK20171027-1.phen.tsv
LINK
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.LBC20180516-2.gwas.tsv
LINK
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.LBC20180516-2.phen.tsv
LINK
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.LBC20180516-3.gwas.tsv
LINK
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.LBC20180516-3.phen.tsv
LINK
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.LBC20180521-1.gwas.tsv
LINK
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.LBC20180521-1.phen.tsv
LINK
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.LBC20180521-5.gwas.tsv
LINK
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.LBC20180521-5.phen.tsv
LINK
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.LBC20180601-3.gwas.tsv
LINK
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.LBC20180601-3.phen.tsv
LINK
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.LBC20180625-2.gwas.tsv
LINK
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.LBC20180625-2.phen.tsv
LINK
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.LBC20180625-3.gwas.tsv
LINK
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.LBC20180625-3.phen.tsv
LINK
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.SST20180209-1.gwas.tsv
LINK
Glycine max GWAS imported from SoyBase.
glyma.mixed.gwas.1W14.SST20180209-1.phen.tsv
LINK
Glycine max gene, protein and mRNA ontology annotations.
glyma.Lee.gnm1.ann1.6NZV.info_annot.txt
LINK
Glycine max gene, protein and mRNA ontology annotations.
glyma.Wm82.gnm1.ann1.DvBy.info_annot.txt
LINK
Glycine max gene, protein and mRNA ontology annotations.
glyma.Wm82.gnm2.ann1.RVB6.info_annot.txt
LINK
Glycine max gene, protein and mRNA ontology annotations.
glyma.Wm82.gnm4.ann1.T8TQ.info_annot.txt
LINK
Glycine max genetic map imported from SoyBase.
glyma.mixed.map.9M0V.GmComposite2003.expt.tsv
LINK
Glycine max genetic map imported from SoyBase.
glyma.mixed.map.9M0V.GmComposite2003.mrk.tsv
LINK
Glycine max genetic map imported from SoyBase.
glyma.mixed.map.9M0V.GmComposite2003.phen.tsv
LINK
Glycine max genetic map imported from SoyBase.
glyma.mixed.map.9M0V.GmComposite2003.qtl.tsv
LINK
Glycine max organism and strain information.
description_Glycine_max.yml
LINK
Glycine max organism and strain information.
strains_Glycine_max.yml
LINK
Glycine soja gene, protein and mRNA ontology annotations.
glyso.PI483463.gnm1.ann1.3Q3Q.info_annot.txt
LINK
Glycine soja organism and strain information.
description_Glycine_soja.yml
LINK
Glycine soja organism and strain information.
strains_Glycine_soja.yml
LINK
LIS datastore genomic FASTA file for Glycine max Lee
glyma.Lee.gnm1.BXNC.genome_main.fna
LINK
LIS datastore genomic FASTA file for Glycine max Wm82.gnm1
glyma.Wm82.gnm1.FCtY.genome_main.fna
LINK
LIS datastore genomic FASTA file for Glycine max Wm82.gnm2
glyma.Wm82.gnm2.DTC4.genome_main.fna
LINK
LIS datastore genomic FASTA file for Glycine max Wm82.gnm4
glyma.Wm82.gnm4.4PTR.genome_main.fna
LINK
LIS datastore genomic FASTA file for Glycine max Zh13
glyma.Zh13.gnm1.N6C8.genome_main.fna
LINK
LIS datastore genomic FASTA file for Glycine soja PI483463
glyso.PI483463.gnm1.YJWS.genome_main.fna
LINK
LIS datastore genomic FASTA file for Glycine soja W05
glyso.W05.gnm1.SVL1.genome_main.fna
LINK
LIS gene families
legume.genefam.fam1.M65K.info_annot_ahrd.tsv
LINK
Plant Reactome pathway assignments for glyma.Lee.gnm1 genes.
glyma.Lee.gnm1.ann1.6NZV.legfed_v1_0.M65K.pathway.tsv
LINK
Plant Reactome pathway assignments for glyma.Wm82.gnm1 genes.
glyma.Wm82.gnm1.ann1.DvBy.legfed_v1_0.M65K.pathway.tsv
LINK
Plant Reactome pathway assignments for glyma.Wm82.gnm2 genes.
glyma.Wm82.gnm2.ann1.RVB6.pathway.tsv
LINK
Plant Reactome pathway assignments for glyma.Wm82.gnm4 genes.
glyma.Wm82.gnm4.ann1.T8TQ.legfed_v1_0.M65K.pathway.tsv
LINK
Plant Reactome pathway assignments for glyma.Zh13.gnm1 genes.
glyma.Zh13.gnm1.ann1.8VV3.legfed_v1_0.M65K.pathway.tsv
LINK
Plant Reactome pathway assignments for glyso.PI483463.gnm1 genes.
glyso.PI483463.gnm1.ann1.3Q3Q.legfed_v1_0.M65K.pathway.tsv
LINK
Plant Reactome pathway assignments for glyso.W05.gnm1 genes.
glyso.W05.gnm1.ann1.T47J.legfed_v1_0.M65K.pathway.tsv
LINK
Protein models for the glyma.Lee.gnm1 genome
glyma.Lee.gnm1.ann1.6NZV.protein_primaryTranscript.faa
LINK
Protein models for the glyma.Wm82.gnm1 genome
glyma.Wm82.gnm1.ann1.DvBy.protein_primaryTranscript.faa
LINK
Protein models for the glyma.Wm82.gnm2 genome
glyma.Wm82.gnm2.ann1.RVB6.protein_primaryTranscript.faa
LINK
Protein models for the glyma.Wm82.gnm4 genome
glyma.Wm82.gnm4.ann1.T8TQ.protein_primaryTranscript.faa
LINK
Protein models for the glyma.Zh13.gnm1 genome
glyma.Zh13.gnm1.ann1.8VV3.protein_primaryTranscript.faa
LINK
Protein models for the glyso.PI483463.gnm1 genome
glyso.PI483463.gnm1.ann1.3Q3Q.protein_primaryTranscript.faa
LINK
Protein models for the glyso.W05.gnm1 genome
glyso.W05.gnm1.ann1.T47J.protein_primaryTranscript.faa
LINK
Soybean gene expression atlas from the Libault Lab.
glyma.Wm82.gnm2.ann1.expr.G7ZY.samples.tsv
LINK
Soybean gene expression atlas from the Libault Lab.
glyma.Wm82.gnm2.ann1.expr.G7ZY.source.tsv
LINK
Soybean gene expression atlas from the Libault Lab.
glyma.Wm82.gnm2.ann1.expr.G7ZY.values.tsv
LINK
Synteny between soybean Wm82.gnm2 and other species.
glyma.Wm82.gnm2.ann1.x.aradu.V14167.gnm1.ann1.gff
LINK
Synteny between soybean Wm82.gnm2 and other species.
glyma.Wm82.gnm2.ann1.x.araip.K30076.gnm1.ann1.gff
LINK
Synteny between soybean Wm82.gnm2 and other species.
glyma.Wm82.gnm2.ann1.x.cajca.ICPL87119.gnm1.ann1.gff
LINK
Synteny between soybean Wm82.gnm2 and other species.
glyma.Wm82.gnm2.ann1.x.lotja.MG20.gnm3.ann1.gff
LINK
Synteny between soybean Wm82.gnm2 and other species.
glyma.Wm82.gnm2.ann1.x.lupan.Tanjil.gnm1.ann1.gff
LINK
Synteny between soybean Wm82.gnm2 and other species.
glyma.Wm82.gnm2.ann1.x.medtr.A17_HM341.gnm4.ann2.gff
LINK
Synteny between soybean Wm82.gnm2 and other species.
glyma.Wm82.gnm2.ann1.x.phavu.G19833.gnm1.ann1.gff
LINK
Synteny between soybean Wm82.gnm2 and other species.
glyma.Wm82.gnm2.ann1.x.phavu.G19833.gnm2.ann1.gff
LINK
Synteny between soybean Wm82.gnm2 and other species.
glyma.Wm82.gnm2.ann1.x.vigan.Gyeongwon.gnm3.ann1.gff
LINK
Synteny between soybean Wm82.gnm2 and other species.
glyma.Wm82.gnm2.ann1.x.vigra.VC1973A.gnm6.ann1.gff
LINK
mRNA models for the glyma.Lee.gnm1 genome
glyma.Lee.gnm1.ann1.6NZV.transcript_primaryTranscript.fna
LINK
mRNA models for the glyma.Wm82.gnm1 genome
glyma.Wm82.gnm1.ann1.DvBy.transcript_primaryTranscript.fna
LINK
mRNA models for the glyma.Wm82.gnm2 genome
glyma.Wm82.gnm2.ann1.RVB6.transcript_primaryTranscript.fna
LINK
mRNA models for the glyma.Wm82.gnm4 genome
glyma.Wm82.gnm4.ann1.T8TQ.transcript_primaryTranscript.fna
LINK
mRNA models for the glyso.PI483463.gnm1 genome
glyso.PI483463.gnm1.ann1.3Q3Q.transcript_primaryTranscript.fna
LINK
PANTHER
PFAM
PIRSF
PRINTS
PROFILE
PROSITE
Plant Ontology
The Plant Ontology (PO) is a community resource consisting of standardized terms, definitions, and logical relations describing plant structures and development stages, augmented by a large database of annotations from genomic and phenomic studies.
Plant Ontology
LINK
Plant Trait Ontology
A controlled vocabulary of describe phenotypic traits in plants.
Plant Trait Ontology
LINK
SFLD
SMART
SSF
Sequence Ontology
The Sequence Ontology is a set of terms and relationships used to describe the features and attributes of biological sequence.
Sequence Ontology
LINK
Soybean Crop Ontology
A controlled vocabulary to describe crop traits in soybean.
Soybean Crop Ontology
LINK
Soybean Growth and Trait Ontology V3.0 revision 1.0
Currently, there are 4 divisions to SOY terms, soybean structural terms (Soybean Structure Ontology), developmental stages (Soybean Developmental Ontology), whole plant development terms (Soybean Whole Plant Growth Stages) and trait terms (Soybean Trait Ontology).
Soybean Growth and Trait Ontology V3.0 revision 1.0
LINK
TIGRFAMs
USDA
Legume Federation
InterMine logo
The Legume Information System (LIS) is a research project of the USDA-ARS:Corn Insects and Crop Genetics Research in Ames, IA.
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